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1 <?xml version="1.0" ?>
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2 <tool id="qiime_fragment-insertion_classify-otus-experimental" name="qiime fragment-insertion classify-otus-experimental" version="2019.4">
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3 <description> - Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime fragment-insertion classify-otus-experimental
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9
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10 --i-representative-sequences=$irepresentativesequences
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11 --i-tree=$itree --o-classification=oclassification
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12
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13
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14 #if str( $id_to_taxonomy_fp.selector ) == 'history'
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15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
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16 --i-reference-taxonomy '$tax'
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17 #else:
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18 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
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19 --i-reference-taxonomy '$tax'
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20 #end if
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21
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22
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23 ;
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24 cp oclassification.qza $oclassification
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25 ]]></command>
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26 <inputs>
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27 <param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences used for a 'sepp' run to produce the 'tree'. [required]" name="irepresentativesequences" optional="False" type="data"/>
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28 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT The tree resulting from inserting fragments into a Phylogeny[Rooted] reference phylogeny, i.e. the output of function 'sepp' [required]" name="itree" optional="False" type="data"/>
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29
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30 <conditional name="id_to_taxonomy_fp" optional="True">
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31 <param name="selector" type="select" label="Reference taxonomy to query">
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32 <option value="cached">Public databases</option>
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33 <option value="history">Databases from your history</option>
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34 </param>
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35 <when value="cached">
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36 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
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37 <options from_data_table="qiime_taxonomy" />
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38 </param>
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39 </when>
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40 <when value="history">
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41 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
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42 </when>
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43 </conditional>
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44
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45 </inputs>
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46 <outputs>
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47 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
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48 </outputs>
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49 <help><![CDATA[
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50 Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.
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51 #######################################################################################
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52
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53 Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID
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54 for every inserted fragment. Then, look up the reference lineage string in
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55 the reference taxonomy.
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56
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57 Parameters
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58 ----------
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59 representative_sequences : FeatureData[Sequence]
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60 The sequences used for a 'sepp' run to produce the 'tree'.
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61 tree : Phylogeny[Rooted]
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62 The tree resulting from inserting fragments into a reference phylogeny,
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63 i.e. the output of function 'sepp'
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64 reference_taxonomy : FeatureData[Taxonomy], optional
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65 Reference taxonomic table that maps every OTU-ID into a taxonomic
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66 lineage string.
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67
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68 Returns
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69 -------
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70 classification : FeatureData[Taxonomy]
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71 Taxonomic lineages for inserted fragments.
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72 ]]></help>
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73 <macros>
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74 <import>qiime_citation.xml</import>
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75 </macros>
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76 <expand macro="qiime_citation"/>
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77 </tool>
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